8JSN

The structure of EBOV L-VP35-RNA complex (conformation 2)

  • Classification: VIRAL PROTEIN/RNA
  • Organism(s): Ebola virus
  • Expression System: Spodoptera
  • Mutation(s): No 

  • Deposited: 2023-06-20 Released: 2023-09-27 
  • Deposition Author(s): Qi, P., Yi, S.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of de novo replication by the Ebola virus polymerase.

Peng, Q.Yuan, B.Cheng, J.Wang, M.Gao, S.Bai, S.Zhao, X.Qi, J.Gao, G.F.Shi, Y.

(2023) Nature 622: 603-610

  • DOI: https://doi.org/10.1038/s41586-023-06608-1
  • Primary Citation of Related Structures:  
    8JSL, 8JSM, 8JSN

  • PubMed Abstract: 

    Non-segmented negative-strand RNA viruses, including Ebola virus (EBOV), rabies virus, human respiratory syncytial virus and pneumoviruses, can cause respiratory infections, haemorrhagic fever and encephalitis in humans and animals, and are considered a substantial health and economic burden worldwide 1 . Replication and transcription of the viral genome are executed by the large (L) polymerase, which is a promising target for the development of antiviral drugs. Here, using the L polymerase of EBOV as a representative, we show that de novo replication of L polymerase is controlled by the specific 3' leader sequence of the EBOV genome in an enzymatic assay, and that formation of at least three base pairs can effectively drive the elongation process of RNA synthesis independent of the specific RNA sequence. We present the high-resolution structures of the EBOV L-VP35-RNA complex and show that the 3' leader RNA binds in the template entry channel with a distinctive stable bend conformation. Using mutagenesis assays, we confirm that the bend conformation of the RNA is required for the de novo replication activity and reveal the key residues of the L protein that stabilize the RNA conformation. These findings provide a new mechanistic understanding of RNA synthesis for polymerases of non-segmented negative-strand RNA viruses, and reveal important targets for the development of antiviral drugs.


  • Organizational Affiliation

    International Institute of Vaccine Research and Innovation (iVac), Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L2,212Ebola virusMutation(s): 0 
Gene Names: L
EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt
Find proteins for A0A1C4HDB0 (Ebola virus)
Explore A0A1C4HDB0 
Go to UniProtKB:  A0A1C4HDB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C4HDB0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase cofactor VP35
B, C, D, E
340Ebola virusMutation(s): 0 
Gene Names: VP35
UniProt
Find proteins for A0A1C4HDK9 (Ebola virus)
Explore A0A1C4HDK9 
Go to UniProtKB:  A0A1C4HDK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C4HDK9
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
The leader sequence of EBOV genomeF [auth G]18Ebola virus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-09-27 
  • Deposition Author(s): Qi, P., Yi, S.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32192452

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references